20th-24th April 2026

To foster international participation, this course will be held online

Epigenetic studies on DNA methylation are now possible to do at the nucleotide level genome-wide and also in non-model organisms. In this course, we will introduce the different available approaches for obtaining and analysing DNA methylation data, including bisulfite sequencing (BS-seq, EM-seq) with Ilumina and long reads with Oxford Nanopore. We will also touch on PacBio long-read analysis. We will cover all necessary steps to obtain methylation information from high throughput data to statistical analyses used to identify differentially methylated sites and regions. The data will be interpreted in terms of their biological importance in the field of ecology and evolution.

The course will be delivered over the course of five days. Each day will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises.

This course is aimed at researchers and technical workers who are or who will be generating and/or analysing DNA methylation from whole genome bisulfite sequencing data from IIlumina, PacBio data or Nanopore data. Examples demonstrated in this course will involve primarily non-model organisms with a draft reference genome available and examples of applications of this data type for different purposes will be covered.

Monday: DNA methylation analysis with short reads (Illumina WGBS and EM-Seq) – 2-7pm Berlin time

-    Presentation: Origin and evolution of DNA methylation in eukaryotes: from parasite defence to gene regulation.
-    Presentation: Introduction to short-read format and processing (WGBS/EM-Seq).
-    Lab 1: Short-read processing:
o    QC, filtering, trimming
o    Genome preparation
o    Alignment, deduplication

Tuesday: DNA methylation analysis with short reads (Illumina WGBS and EM-Seq) – 2-7pm Berlin time

-    Presentation: Introduction to DNAm in plants.
-    Presentation: Population epigenomics: patterns and drivers of DNAm variation in natural populations.
-    Lab 2: Short-read processing:
o    Conversion efficiencies (lambda/pUC19)
o    Methylation count files
o    Accounting for SNPs

Wednesday: DNA methylation analysis with long reads (Oxford Nanopore) – 2-7pm Berlin time

-    Presentation: Nuances of DNA methylation data: sex, tissue, age, imprinting and allelic-variation.
-    Presentation: Introduction to long-read format and processing (Nanopore/PacBio).
-    Lab 3: Nanopore long-read processing:
o    Fast5/pod5 generation, Pod5 tools
o    Dorado/Guppy, and models
o    Modbam2bed/Modkit
o    Example: methylation haplophasing

Thursday: Identification of differentially methylated sites and regions and integration with SNP data – 2-7pm Berlin time

-    Presentation: DNAm and genetic variation: biological insights and analytical hazards.
-    Presentation: Introduction to differential DNA methylation.
-    Lab 4: Differential DNA methylation:
o    Testing for differentially methylated sites and regions between populations and conditions
o    Visualising differential methylation
o    Accounting for SNPs

Friday: Integration of DNA methylation and gene expression and open session on your own data / experiments – 2-7pm Berlin time
-    Lab 5: Integration of DNA methylation and gene expression:
o    Quantifying genes/exon/intron levels
o    Correlational plots
o    Overlap of differential methylation and differential expression
-    Open session: Group questions / discussion:
o    Follow up on any course material
o    Student questions on their own data / experimental plans

Instructors

1- Epigenomics - ONLINE, 13-17 April

2- Gene Set Enrichment Analysis in R - ONLINE, 11-15 May

3- RNAseq for beginners - ONLINE, 19th-28th of May